Package org.neuroml.model.util

Class CellUtils

java.lang.Object

org.neuroml.model.util.CellUtils

public class CellUtils
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static String	NEUROML2_NEUROLEX_UNBRANCHED_NONOVERLAPPING_SEG_GROUP

Constructor Summary

Constructors

Constructor	Description
CellUtils()

Method Summary

Modifier and Type	Method	Description
static double	distance(Point3DWithDiam p, Point3DWithDiam d)
static BiophysicalProperties	getCellBiophysicalProperties(Cell cell, NeuroMLDocument nml2doc)
static Morphology	getCellMorphology(Cell cell, NeuroMLDocument nml2doc)
static double	getFractionAlongSegGroupLength(Cell cell, String segmentGroup, int segmentId, float fractAlongSegment)
static double	getFractionAlongSegGroupLength(Cell cell, NeuroMLDocument nml2doc, String segmentGroup, int segmentId, float fractAlongSegment)
static LinkedHashMap<Integer,Segment>	getIdsVsSegments(Cell cell)	Deprecated. use getIdsVsSegments(Cell cell, NeuroMLDocument nml2doc) instead.
static LinkedHashMap<Integer,Segment>	getIdsVsSegments(Cell cell, NeuroMLDocument nml2doc)
static LinkedHashMap<String,SegmentGroup>	getNamesVsSegmentGroups(Cell cell)
static LinkedHashMap<String,SegmentGroup>	getNamesVsSegmentGroups(Cell cell, NeuroMLDocument nml2doc)
static SegmentGroup	getSegmentGroup(Cell cell, String id)
static LinkedHashMap<SegmentGroup,ArrayList<Integer>>	getSegmentGroupsVsSegIds(Cell cell)
static LinkedHashMap<SegmentGroup,ArrayList<Integer>>	getSegmentGroupsVsSegIds(Cell cell, NeuroMLDocument nml2doc)
static ArrayList<Integer>	getSegmentIdsInGroup(LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups, SegmentGroup segmentGroup)
static ArrayList<Integer>	getSegmentIdsInGroup(Cell cell, String segmentGroup)
static ArrayList<Segment>	getSegmentsInGroup(Cell cell, String segmentGroup)	Deprecated.
static ArrayList<Segment>	getSegmentsInGroup(Cell cell, LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups, SegmentGroup segmentGroup)
static ArrayList<Segment>	getSegmentsInGroup(Cell cell, NeuroMLDocument nml2doc, String segmentGroup)
static ArrayList<Segment>	getSegmentsInGroup(Cell cell, NeuroMLDocument nml2doc, LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups, SegmentGroup segmentGroup)
static Segment	getSegmentWithId(Cell cell, int segmentId)	Deprecated.
static Segment	getSegmentWithId(Cell cell, NeuroMLDocument nml2doc, int segmentId)
static boolean	hasSegmentGroup(Cell cell, String segmentGroup)
static boolean	hasUnbranchedNonOverlappingInfo(Cell cell)	Deprecated.
static boolean	hasUnbranchedNonOverlappingInfo(Cell cell, NeuroMLDocument nml2doc)
static boolean	isUnbranchedNonOverlapping(SegmentGroup sg)
static void	main(String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

NEUROML2_NEUROLEX_UNBRANCHED_NONOVERLAPPING_SEG_GROUP

public static String NEUROML2_NEUROLEX_UNBRANCHED_NONOVERLAPPING_SEG_GROUP

Constructor Details

CellUtils

public CellUtils()

Method Details

isUnbranchedNonOverlapping

public static boolean isUnbranchedNonOverlapping(SegmentGroup sg)

hasUnbranchedNonOverlappingInfo

@Deprecated
public static boolean hasUnbranchedNonOverlappingInfo(Cell cell)
                                               throws NeuroMLException

Deprecated.

Throws:

NeuroMLException

hasUnbranchedNonOverlappingInfo

public static boolean hasUnbranchedNonOverlappingInfo(Cell cell,
 NeuroMLDocument nml2doc)
                                               throws NeuroMLException

Throws:

NeuroMLException

getCellMorphology

public static Morphology getCellMorphology(Cell cell,
 NeuroMLDocument nml2doc)
                                    throws NeuroMLException

Throws:

NeuroMLException

getCellBiophysicalProperties

public static BiophysicalProperties getCellBiophysicalProperties(Cell cell,
 NeuroMLDocument nml2doc)

getIdsVsSegments

@Deprecated
public static LinkedHashMap<Integer,Segment> getIdsVsSegments(Cell cell)

Deprecated.

use getIdsVsSegments(Cell cell, NeuroMLDocument nml2doc) instead.

getIdsVsSegments

public static LinkedHashMap<Integer,Segment> getIdsVsSegments(Cell cell,
 NeuroMLDocument nml2doc)
                                                       throws NeuroMLException

Throws:

NeuroMLException

getSegmentGroup

public static SegmentGroup getSegmentGroup(Cell cell,
 String id)
                                    throws NeuroMLException

Throws:

NeuroMLException

getSegmentWithId

@Deprecated
public static Segment getSegmentWithId(Cell cell,
 int segmentId)
                                throws NeuroMLException

Deprecated.

Throws:

NeuroMLException

getSegmentWithId

public static Segment getSegmentWithId(Cell cell,
 NeuroMLDocument nml2doc,
 int segmentId)
                                throws NeuroMLException

Throws:

NeuroMLException

getNamesVsSegmentGroups

public static LinkedHashMap<String,SegmentGroup> getNamesVsSegmentGroups(Cell cell,
 NeuroMLDocument nml2doc)
                                                                  throws NeuroMLException

Throws:

NeuroMLException

getNamesVsSegmentGroups

public static LinkedHashMap<String,SegmentGroup> getNamesVsSegmentGroups(Cell cell)
                                                                  throws NeuroMLException

Throws:

NeuroMLException

getSegmentIdsInGroup

public static ArrayList<Integer> getSegmentIdsInGroup(Cell cell,
 String segmentGroup)
                                               throws NeuroMLException

Throws:

NeuroMLException

getSegmentIdsInGroup

public static ArrayList<Integer> getSegmentIdsInGroup(LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups,
 SegmentGroup segmentGroup)

hasSegmentGroup

public static boolean hasSegmentGroup(Cell cell,
 String segmentGroup)

getSegmentsInGroup

@Deprecated
public static ArrayList<Segment> getSegmentsInGroup(Cell cell,
 String segmentGroup)
                                             throws NeuroMLException

Deprecated.

Throws:

NeuroMLException

getSegmentsInGroup

public static ArrayList<Segment> getSegmentsInGroup(Cell cell,
 NeuroMLDocument nml2doc,
 String segmentGroup)
                                             throws NeuroMLException

Throws:

NeuroMLException

getSegmentsInGroup

public static ArrayList<Segment> getSegmentsInGroup(Cell cell,
 LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups,
 SegmentGroup segmentGroup)
                                             throws NeuroMLException

Throws:

NeuroMLException

getSegmentsInGroup

public static ArrayList<Segment> getSegmentsInGroup(Cell cell,
 NeuroMLDocument nml2doc,
 LinkedHashMap<String,SegmentGroup> namesVsSegmentGroups,
 SegmentGroup segmentGroup)
                                             throws NeuroMLException

Throws:

NeuroMLException

getSegmentGroupsVsSegIds

public static LinkedHashMap<SegmentGroup,ArrayList<Integer>> getSegmentGroupsVsSegIds(Cell cell)
                                                                               throws NeuroMLException

Throws:

NeuroMLException

getSegmentGroupsVsSegIds

public static LinkedHashMap<SegmentGroup,ArrayList<Integer>> getSegmentGroupsVsSegIds(Cell cell,
 NeuroMLDocument nml2doc)
                                                                               throws NeuroMLException

Throws:

NeuroMLException

distance

public static double distance(Point3DWithDiam p,
 Point3DWithDiam d)

getFractionAlongSegGroupLength

public static double getFractionAlongSegGroupLength(Cell cell,
 String segmentGroup,
 int segmentId,
 float fractAlongSegment)
                                             throws NeuroMLException

Throws:

NeuroMLException

getFractionAlongSegGroupLength

public static double getFractionAlongSegGroupLength(Cell cell,
 NeuroMLDocument nml2doc,
 String segmentGroup,
 int segmentId,
 float fractAlongSegment)
                                             throws NeuroMLException

Throws:

NeuroMLException

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception